[gmx-users] pulling protein-ligand complex

[Justin Lemkul]

On 1/15/17 12:59 AM, abhisek Mondal wrote:
> I think I would prefer 'pull-vector' approach given my system's property.
> Do we have any program to calculate this COM difference and formulate a
> pull-path ? Can you please give me any paper where this process is
> used/explained in detail ? I have seen you paper in JPC B but I guess
> protein-ligand gives a different scenario. Ligands generally found to be
> trapped in a complex manner inside protein's binding cleft.
>

Thus you have to figure out the appropriate path for the ligand to exit based on 
the geometry of the protein.  If there's a clear exit channel, compute the COM 
of, e.g. residues interacting the the ligand and those defining the exit of the 
channel.  The vector is simply the distance between those two COM positions, so 
you don't need a program, you need a four-function calculator :)

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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